fix: max_v flag initial value

src/Makefile

@@ -4,6 +4,13 @@ CFLAGS= -I. -O2 -ffast-math -O3 -fopenmp -std=c++11
 Sanity: calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
 	$(CC) $(CFLAGS) -o ../bin/Sanity calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
 
+Sanity_lib: CFLAGS += -fPIC
+Sanity_lib: libSanity.a
+
+libSanity.a: calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
+	ar rcs libSanity.a calc_true_variation_parallel_prior_mu_sigma.o ReadInputFiles.o FitFrac.o FukushimaLambertW.o Digamma_Trigamma.o
+	cp libSanity.a ../../
+
 calc_true_variation_parallel_prior_mu_sigma.o: calc_true_variation_parallel_prior_mu_sigma.cpp ReadInputFiles.h FitFrac.h FukushimaLambertW.h Digamma_Trigamma.h
 	$(CC) $(CFLAGS) -c calc_true_variation_parallel_prior_mu_sigma.cpp
 

src/calc_true_variation_parallel_prior_mu_sigma.cpp

@@ -755,7 +755,7 @@ void parse_argv(int argc,char** argv, string &in_file, string &gene_name_file, s
 	int N_param(11);
 	string extended_output("false");
 	string no_norm_str("false");
-	string max_v_str("true");
+	string max_v_str("false");
     string to_find[11][2] = {{"-f", "--file"},
 							{"-d", "--destination"},
 							{"-n", "--n_threads"},

src/calc_true_variation_parallel_prior_mu_sigma.h

@@ -0,0 +1,11 @@
+/* NOTES:
+   - this function gets posterior estimates for a single gene
+   - mu/var_mu is library-corrected log mean expression
+   - delta/var_delta is library-corrected guassian noise for log mean expression (e.g. gaussian noise for rate)
+   - variables with _ml are guassian bin with the highest likelhood
+    - posterior is a mixture of guassian distributions
+    - the regular version computes weighted average of those guassian distributions
+   - N_c is the observed libsize
+   - n_c is the observed gene counts for a specific gene
+*/
+void get_gene_expression_level(double *n_c, double *N_c, double n, double vmin, double vmax, double &mu, double &var_mu, double *delta, double *var_delta, int C, int numbin, double a, double b, double *lik, double &v_ml, double &mu_v_ml, double &var_mu_v_ml, double *delta_v_ml, double *var_delta_v_ml);